====== Help DRIMM ======

This program is dedicated to the estimation and the use of Drifting Markov Models (DMM).

===== Two different ways to use =====


  - DMM is estimated on a sequence.
  - DMM is given in a model file.

===== Description of parameters =====

** -SpM ** Estimation by splines M. -N must be used.\\

**-SpH ** Estimation by splines H. -N and -Nar must be used.

**-Spl** Estimation by splines. -N and -Nar must be used.

**-Poly** Estimation by polynom (stochastic matrices).

** -PolyM** Estimation by polynom (no stochastic matrices).

** -out <basename> ** Basename for all output files. Output 'basename.config_<num>.out' with -s.  Output 'basename.config_sm.out' with -sm. Output 'basename.config_ss.out' with -ss. Output 'basename.config.out' with -cf.

** -a <alphabet_file> ** A file describing the alphabet to use.

**-s <sequence_file>**A file containing file of sequences. DMM is estimated on each sequence (Use 1). At least one of -s or -sm or -ss must be used

**-sm <sequence_mean_file>** A file containing file of sequences. DMM is estimated as a mean of DDM on each sequence (Use 1). At least one of -s or -sm or -ss must be used


** -ss <sequence_sum_file> **A file containing file of sequences. DMM is estimated over all the sequences (Use 1). At least one of -s or -sm or -ss must be used

** -order <order>=0>**Order of the DMM (Use 1). Order must be > 0 with -SpM or -SpH.

** -deg <degree>=0> ** Degree of the DMM (Use 1). Degree is useless with -SpH and -Spl. Degree is 3.

**-N <Number of segments>0> ** Number of segments in the case of estimation by splines.

**-Nar <Number of segments>0> ** Number of aller retour with -Spl and -SpH.

**-cf <model_file> ** DMM is given by the <model_file> (Use 2). Must be used with -Poly, -PolyM, -Spl, -SpM, or -SpH.

** -L  ** Compute the log-likelihood on the estimated sequences (Use 1). Can not be used with -sm or -ss

**-AIC **Compute the AIC on the estimated sequences (Use 1). Can not be used with -sm or -ss

**-BIC  **Compute the BIC on the estimated sequences (Use 1). Can not be used with -sm or -ss

**-l <sequence_file_l> **Compute the log-likelihood on <sequence_file_l>.

**-aic <sequence_file_aic>**Compute the aic on <sequence_file_aic>.

**-bic <sequence_file_bic> ** Compute the bic on <sequence_file_bic>.

**-law **Compute the stationary law of the DMM. basename.trace_stat_<num>.out is an output containing the stationary law. <num> is an integer designing the number of the sequence.


**-slaw <in>0> <out>0> ** Compute the stationary law of the DMM between <in> and <out>. basename.trace_stat_segment_<num>.out is an output containing the stationary law. <num> is an integer designing the number of the sequence.


**-dist ** Compute distributions of the DMM. basename.trace_dist_<num>.out is an output containing the distributions. <num> is an integer designing the number of the sequence.


**sdist <in>0> <out>0>** Compute the distribution of the DMM between <in> and <out>. basename.trace_dist_segment_<num>.out is an output containing the distributions. <num> is an integer designing the number of the sequence.


**-pi ** Return files 'basename.Pit_<num>.out' or 'basename.Pit_sm.out' or basename.Pit.out' or 'basename.Pit_ss.out' containing the matrix Pi_t for all t. <num> is an integer designing the number of the sequence


**-simu** Return files 'basename.simulation_<num>.out' or 'basename.simulation_sm.out' or 'basename.simulation_ss.out' or basename.simulation.out' containing a sequence simulated by the DMM. <num> is an integer designing the number of the sequence.

**-nv** Mode 'not verbose'.

**-h ** Print this help.

===== Examples =====

  DRIMM -Poly -order 1 -deg 2 -a dna.alpha -s lambda.fa -out lambda

for the estimation of a polynomial DMM (order 1 and degree 2) on the phage Lambda.

  DRIMM -SpM -N 2 -order 1 -deg 3 -a dna.alpha -s lambda.fa -out lambda


for the estimation of a DMM with polynomial splines (order 1 and degree 3 with 2 segments) on the phage Lambda.